Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

STACK: Sequence Tag Alignment and Consensus Knowledgebase.

A Christoffels1, A van Gelder, G Greyling

  • 1South African National Bioinformatics Institute, Private Bag X17, Bellville 7535, University of Western Cape, South Africa.

Nucleic Acids Research
|January 11, 2000
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Cough as a clinical manifestation of giant cell arteritis.

Scandinavian journal of rheumatology·2026
Same author

Online coupling of thermal field-flow fractionation and Fourier transform infrared spectroscopy as a powerful tool for polymer characterization.

Journal of chromatography. A·2018
Same author

Core microstructure, morphology and chain arrangement of block copolymer self-assemblies as investigated by thermal field-flow fractionation.

Journal of chromatography. A·2018
Same author

Exploring the potential of T7 bacteriophage protein Gp2 as a novel inhibitor of mycobacterial RNA polymerase.

Tuberculosis (Edinburgh, Scotland)·2017
Same author

Optimization of Ordered Subset Expectation Maximization Reconstruction for Reducing Urinary Bladder Artifacts in Single-photon Emission Computed Tomography Imaging.

World journal of nuclear medicine·2011
Same author

[Occupational dermatitis in veterinarians].

Tijdschrift voor diergeneeskunde·2008
Same journal

Correction to 'scSuperAnnotator: A platform for benchmarking comparison and visualizing automated cellular annotation methods for scRNA-seq data'.

Nucleic acids research·2026
Same journal

Correction to 'Differentiable partition function calculation for RNA'.

Nucleic acids research·2026
Same journal

Deployment of non-canonical splicing in tunicate genomes is mediated by divergent U2AF function and changing m6A modification in U1 and U6 snRNA.

Nucleic acids research·2026
Same journal

Bacillus subtilis DnaB forms multiple protein-protein interactions essential for DNA replication initiation.

Nucleic acids research·2026
Same journal

Multiple forms of protein-protein and DNA binding are exhibited by BrxC from the BREX phage restriction system.

Nucleic acids research·2026
Same journal

Biosynthesis of glycosylated 5-hydroxycytosine in the DNA of diverse viruses.

Nucleic acids research·2026
See all related articles

STACK is a novel tool for analyzing human transcript variations across developmental and pathological states. It reconstructs and visualizes transcript data from public resources, offering insights into gene expression.

Area of Science:

  • Bioinformatics
  • Genomics
  • Molecular Biology

Background:

  • Understanding human transcript variation is crucial for studying gene expression in health and disease.
  • Existing gene indexing projects often rely on pairwise alignment, limiting their ability to capture diverse transcript variants.

Purpose of the Study:

  • To introduce STACK, a tool for detecting and visualizing expressed transcript variation.
  • To organize and reconstruct human transcripts from public data, contextualizing expression states.
  • To provide a comprehensive resource for exploring transcript diversity and its relation to developmental and pathological conditions.

Main Methods:

  • STACK reconstructs human transcripts by clustering expressed sequence tag (EST) data.
  • A novel clustering approach tolerates sub-sequence diversity without relying on pairwise alignment.

Related Experiment Videos

  • The system processes all publicly available human EST data from GenBank at least four times annually.

    • Main Results:

    • STACK generates consensus transcripts that reflect transcript diversity.
    • The tool enables visualization of transcript variation in developmental and pathological contexts.
    • Processed information is accessible through tissue-specific, disease-related, and whole-body indices.

    Conclusions:

    • STACK offers a unique resource for transcriptomic analysis by reconstructing transcript databases.
    • The associated generation tools are also publicly available, promoting broad applicability.
    • This approach enhances the capture of transcript variants compared to traditional methods.